Multiple sequence alignment - TraesCS5D01G539000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)



BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G539000 chr5D 100.000 2742 0 0 1 2742 550659636 550662377 0.000000e+00 5064.0
1 TraesCS5D01G539000 chr5D 87.579 475 32 10 1457 1913 551024827 551025292 2.420000e-145 525.0
2 TraesCS5D01G539000 chr5D 92.881 295 20 1 535 829 551024321 551024614 7.020000e-116 427.0
3 TraesCS5D01G539000 chr5D 82.546 487 49 30 708 1178 550965247 550965713 1.980000e-106 396.0
4 TraesCS5D01G539000 chr5D 87.379 309 23 10 1535 1831 550646697 550647001 9.400000e-90 340.0
5 TraesCS5D01G539000 chr5D 94.089 203 12 0 973 1175 551024624 551024826 2.650000e-80 309.0
6 TraesCS5D01G539000 chr5D 85.397 315 24 12 1535 1833 550965795 550966103 9.540000e-80 307.0
7 TraesCS5D01G539000 chr5D 90.476 210 16 3 973 1178 550964698 550964907 9.670000e-70 274.0
8 TraesCS5D01G539000 chr5D 90.972 144 13 0 666 809 550964516 550964659 7.750000e-46 195.0
9 TraesCS5D01G539000 chr5D 82.710 214 18 11 598 793 550646134 550646346 3.630000e-39 172.0
10 TraesCS5D01G539000 chr5D 100.000 36 0 0 2588 2623 267843574 267843539 1.760000e-07 67.6
11 TraesCS5D01G539000 chr7B 93.548 496 25 5 1 490 96400919 96400425 0.000000e+00 732.0
12 TraesCS5D01G539000 chr7B 92.369 498 28 9 1 490 720142933 720142438 0.000000e+00 701.0
13 TraesCS5D01G539000 chr7B 89.076 119 13 0 826 944 17664989 17665107 6.120000e-32 148.0
14 TraesCS5D01G539000 chr7A 93.293 492 27 6 1 490 720724559 720725046 0.000000e+00 721.0
15 TraesCS5D01G539000 chr7A 81.618 544 76 17 2057 2585 287210876 287210342 1.950000e-116 429.0
16 TraesCS5D01G539000 chr7A 89.046 283 28 3 1177 1457 533624314 533624033 5.620000e-92 348.0
17 TraesCS5D01G539000 chr7D 92.323 508 29 7 1 500 617769775 617769270 0.000000e+00 713.0
18 TraesCS5D01G539000 chr7D 92.008 513 29 9 1 504 501611010 501610501 0.000000e+00 710.0
19 TraesCS5D01G539000 chr3D 93.075 491 26 7 4 490 254459725 254459239 0.000000e+00 712.0
20 TraesCS5D01G539000 chr3D 90.323 279 25 2 1182 1459 460121078 460120801 5.580000e-97 364.0
21 TraesCS5D01G539000 chr3D 90.323 279 25 2 1182 1459 525540947 525541224 5.580000e-97 364.0
22 TraesCS5D01G539000 chr3D 89.720 107 10 1 2057 2162 538630459 538630565 4.760000e-28 135.0
23 TraesCS5D01G539000 chr3D 89.796 98 10 0 1948 2045 609900474 609900377 2.870000e-25 126.0
24 TraesCS5D01G539000 chr5B 92.292 506 29 7 1 502 47330517 47331016 0.000000e+00 710.0
25 TraesCS5D01G539000 chr5B 89.614 414 23 7 1537 1931 703306144 703306556 2.440000e-140 508.0
26 TraesCS5D01G539000 chr5B 92.881 295 19 2 535 829 703305548 703305840 7.020000e-116 427.0
27 TraesCS5D01G539000 chr5B 88.856 341 26 9 1484 1816 703271752 703272088 2.540000e-110 409.0
28 TraesCS5D01G539000 chr5B 91.582 297 21 3 535 829 703291311 703291605 9.140000e-110 407.0
29 TraesCS5D01G539000 chr5B 89.716 282 28 1 1181 1461 308836452 308836171 2.600000e-95 359.0
30 TraesCS5D01G539000 chr5B 88.487 304 21 10 1535 1831 703269012 703269308 3.360000e-94 355.0
31 TraesCS5D01G539000 chr5B 87.372 293 23 8 1535 1816 703291895 703292184 9.470000e-85 324.0
32 TraesCS5D01G539000 chr5B 95.074 203 10 0 973 1175 703305846 703306048 1.230000e-83 320.0
33 TraesCS5D01G539000 chr5B 92.271 207 15 1 973 1178 703291615 703291821 2.670000e-75 292.0
34 TraesCS5D01G539000 chr5B 89.806 206 18 1 973 1175 703271533 703271738 7.530000e-66 261.0
35 TraesCS5D01G539000 chr5B 89.831 118 12 0 827 944 413048759 413048876 4.730000e-33 152.0
36 TraesCS5D01G539000 chr2B 92.137 496 32 6 1 490 776895632 776895138 0.000000e+00 693.0
37 TraesCS5D01G539000 chr2B 91.984 499 30 8 1 494 707594573 707594080 0.000000e+00 691.0
38 TraesCS5D01G539000 chr2B 89.643 280 26 3 1182 1459 133123230 133122952 1.210000e-93 353.0
39 TraesCS5D01G539000 chr2B 89.831 118 12 0 826 943 274594728 274594845 4.730000e-33 152.0
40 TraesCS5D01G539000 chr2B 88.525 122 13 1 827 948 222094682 222094562 2.200000e-31 147.0
41 TraesCS5D01G539000 chr3B 80.146 549 81 20 2056 2585 475253745 475253206 4.280000e-103 385.0
42 TraesCS5D01G539000 chr3B 78.425 292 49 7 2305 2583 706734829 706734539 7.800000e-41 178.0
43 TraesCS5D01G539000 chr4B 80.337 534 77 19 2071 2585 478573311 478572787 1.990000e-101 379.0
44 TraesCS5D01G539000 chr4B 88.929 280 30 1 1182 1460 37402791 37402512 7.270000e-91 344.0
45 TraesCS5D01G539000 chr4B 90.698 43 4 0 2056 2098 482641496 482641454 1.060000e-04 58.4
46 TraesCS5D01G539000 chr6B 89.085 284 30 1 1177 1459 207461891 207462174 4.340000e-93 351.0
47 TraesCS5D01G539000 chr6B 89.007 282 30 1 1181 1461 588947958 588948239 5.620000e-92 348.0
48 TraesCS5D01G539000 chr1B 89.007 282 28 3 1181 1461 522523692 522523413 2.020000e-91 346.0
49 TraesCS5D01G539000 chr1B 78.311 521 84 16 2082 2584 5275950 5276459 2.650000e-80 309.0
50 TraesCS5D01G539000 chr1B 88.983 118 13 0 827 944 292419249 292419366 2.200000e-31 147.0
51 TraesCS5D01G539000 chr4A 87.667 300 27 8 1538 1831 616977492 616977197 9.400000e-90 340.0
52 TraesCS5D01G539000 chr4A 91.892 222 13 2 1538 1754 616961551 616961330 3.430000e-79 305.0
53 TraesCS5D01G539000 chr4A 79.616 417 71 13 2063 2473 36070921 36070513 1.240000e-73 287.0
54 TraesCS5D01G539000 chr4A 77.170 530 76 26 2071 2585 669402192 669402691 1.620000e-67 267.0
55 TraesCS5D01G539000 chr4A 92.090 177 6 3 535 704 616918702 616918527 2.730000e-60 243.0
56 TraesCS5D01G539000 chr4A 80.220 273 21 18 570 829 616962125 616961873 1.010000e-39 174.0
57 TraesCS5D01G539000 chr4A 90.678 118 11 0 826 943 660676626 660676743 1.020000e-34 158.0
58 TraesCS5D01G539000 chr4A 90.000 120 12 0 826 945 687422431 687422550 3.660000e-34 156.0
59 TraesCS5D01G539000 chr4A 79.012 243 21 17 582 809 616978045 616977818 3.680000e-29 139.0
60 TraesCS5D01G539000 chr1D 78.889 540 87 16 2062 2584 169699 169170 9.400000e-90 340.0
61 TraesCS5D01G539000 chr1D 94.737 38 2 0 2587 2624 259209479 259209516 2.950000e-05 60.2
62 TraesCS5D01G539000 chr5A 80.189 424 72 11 2053 2472 390376244 390375829 9.540000e-80 307.0
63 TraesCS5D01G539000 chr5A 86.139 101 14 0 1946 2046 480099061 480098961 2.890000e-20 110.0
64 TraesCS5D01G539000 chrUn 79.419 413 67 14 2057 2460 27877855 27878258 2.690000e-70 276.0
65 TraesCS5D01G539000 chrUn 81.915 282 47 3 2056 2337 42512639 42512362 4.560000e-58 235.0
66 TraesCS5D01G539000 chr2D 88.983 118 13 0 827 944 376048231 376048114 2.200000e-31 147.0
67 TraesCS5D01G539000 chr3A 86.139 101 14 0 1946 2046 593037324 593037224 2.890000e-20 110.0
68 TraesCS5D01G539000 chr3A 94.595 37 2 0 2057 2093 714534018 714533982 1.060000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G539000 chr5D 550659636 550662377 2741 False 5064.000000 5064 100.000000 1 2742 1 chr5D.!!$F1 2741
1 TraesCS5D01G539000 chr5D 551024321 551025292 971 False 420.333333 525 91.516333 535 1913 3 chr5D.!!$F4 1378
2 TraesCS5D01G539000 chr5D 550964516 550966103 1587 False 293.000000 396 87.347750 666 1833 4 chr5D.!!$F3 1167
3 TraesCS5D01G539000 chr5D 550646134 550647001 867 False 256.000000 340 85.044500 598 1831 2 chr5D.!!$F2 1233
4 TraesCS5D01G539000 chr7A 287210342 287210876 534 True 429.000000 429 81.618000 2057 2585 1 chr7A.!!$R1 528
5 TraesCS5D01G539000 chr7D 617769270 617769775 505 True 713.000000 713 92.323000 1 500 1 chr7D.!!$R2 499
6 TraesCS5D01G539000 chr7D 501610501 501611010 509 True 710.000000 710 92.008000 1 504 1 chr7D.!!$R1 503
7 TraesCS5D01G539000 chr5B 703305548 703306556 1008 False 418.333333 508 92.523000 535 1931 3 chr5B.!!$F5 1396
8 TraesCS5D01G539000 chr5B 703269012 703272088 3076 False 341.666667 409 89.049667 973 1831 3 chr5B.!!$F3 858
9 TraesCS5D01G539000 chr5B 703291311 703292184 873 False 341.000000 407 90.408333 535 1816 3 chr5B.!!$F4 1281
10 TraesCS5D01G539000 chr3B 475253206 475253745 539 True 385.000000 385 80.146000 2056 2585 1 chr3B.!!$R1 529
11 TraesCS5D01G539000 chr4B 478572787 478573311 524 True 379.000000 379 80.337000 2071 2585 1 chr4B.!!$R2 514
12 TraesCS5D01G539000 chr1B 5275950 5276459 509 False 309.000000 309 78.311000 2082 2584 1 chr1B.!!$F1 502
13 TraesCS5D01G539000 chr4A 616961330 616962125 795 True 239.500000 305 86.056000 570 1754 2 chr4A.!!$R3 1184
14 TraesCS5D01G539000 chr4A 616977197 616978045 848 True 239.500000 340 83.339500 582 1831 2 chr4A.!!$R4 1249
15 TraesCS5D01G539000 chr1D 169170 169699 529 True 340.000000 340 78.889000 2062 2584 1 chr1D.!!$R1 522


AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
840 1575 0.098376 CCTCGTACTCCTTCCGTTCG 59.902 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 3672 0.031314 CACGATCGATGGAGTGGGAG 59.969 60.0 24.34 0.0 0.0 4.3 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)



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AutoCloner maintained by Alex Coulton.